I'm thinking about putting in a cap for better clarity at high volume levels. Can anyone recommend something decent that will help? And where in the circuit do I install it? I have a Sony Xplod head, 300W alpine, two 1100w 12's, two 6x9's, and two 6 1/2's. Thanks!

In a good electrical system and with properly designed amplifiers an external cap isn't really necessary. The lack of clarity is probably due to either the amps clipping or the load on your speakers, car audio speakers can rarely take the wattage they claim.

The only place a cap would help you with that system is right next to the amp that is powering the subwoofers. It should be within 6 inches of that amp. What the cap does... it will cause less voltage dips on hard hitting bass. (if your amp can supply that) Usually alpine amps are very efficient.
The advantages... -some of these are a stretch...
more consistent voltage through out the entire car. (you might notice your headlights stop dimming)
better running car... ie more voltage to the coil...
longer life on the alternator...
Better sounding stereo... ie if your sub amp was causing a voltage drain that could cause less voltaged to the head unit... which in turn raises your Total Harmonic Distortion ie THD...

I used to run 2 accuvolt 1400 .. I had them set to 14.4 volts.. it made a world of difference because the amps gained about 20% power rather then running them at 11.5 - 12.5 volts... anyway
I digress...

I really wouldn't waste money on a cap though if I was you...
I would by a battery isolator and run a secondary battery for your radio.